Re: [chimerax-users] labelling hbond atoms
Dear Group,
I have a possibly rookie level question.
When i use name flag with hbonds command to define two groups of hbonds like this
hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1
hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2
then when i try to label the hbond atoms ,
la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20
I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this.
welcome to hear your suggestions.
thanks again., amith
Dear Amith, The "hbondatoms" specifier only works for the default h-bond model name, "hydrogen bonds": https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin
Instead you can use "select true" and then label the selected atoms, e.g.:
hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1 select true la sel residues font "Rockwell Extra Bold" height .6 bg 20,20,20 hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2 select true la sel residues font "Rockwell Extra Bold" height .6 bg 20,20,20
https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html
A few other things about your hbonds commands:
(1) you could just use #1.2 instead of #1.2.* -- the first one specifies everything under #1.2
(2) my tests suggest you also need to add the "interSubmodel true" option to your commands find any hbonds. However, this may be be due to my test only having a #1.2 model, not sub-submodels of #1.2.
I also see that "hbonds delete HBONDS-1" does not work even though the model name is indeed HBONDS-1 as shown in the Model Panel. This may be a bug, but you can still close the model just using the Model Panel or the "close" command.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 13, 2021, at 8:52 PM, Rangarajan, Amith via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Group, I have a possibly rookie level question. When i use name flag with hbonds command to define two groups of hbonds like this
hbonds (#1.1 & protein) restrict (#1.2.* ) distslop .2 reveal t rad .2 color gold name HBONDS-1
hbonds(#1.1 & ~protein) restrict(#1.2.*) distslop .2 reveal t rad .2 color magenta name HBONDS-2
then when i try to label the hbond atoms ,
la hbondatoms residues font "Rockwell Extra Bold" height .6 bg 20,20,20
I am not getting the labels. I am not getting any errors so i figured that it got to do with hbonds being given a name , however i am not able to fix this. welcome to hear your suggestions. thanks again., amith
On Oct 14, 2021, at 9:00 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
I also see that "hbonds delete HBONDS-1" does not work even though the model name is indeed HBONDS-1 as shown in the Model Panel. This may be a bug, but you can still close the model just using the Model Panel or the "close" command.
This is fixed in tomorrow's daily build.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
participants (3)
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Elaine Meng
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Eric Pettersen
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Rangarajan, Amith